弦图，管他中不中用，反正高大上

0.准备输入数据

可以是矩阵

library(circlize)
set.seed(999)
mat = sample(0:5,21,replace = T)
mat = matrix(mat,nrow = 3)
rownames(mat) = paste0("S",1:nrow(mat))
colnames(mat) = paste0("G",1:ncol(mat))
mat

##    G1 G2 G3 G4 G5 G6 G7
## S1  2  0  1  2  5  1  2
## S2  3  5  1  4  2  0  1
## S3  4  0  5  5  2  4  3

行是一边，列是一边，矩阵正文的数字表示连接的强度。

可以是tidy数据框

library(tidyr)
library(tibble)
df <- gather(rownames_to_column(as.data.frame(mat),var = "from"),
             key = "to",
             value = "value",
             - from)
head(df)

##   from to value
## 1   S1 G1     2
## 2   S2 G1     3
## 3   S3 G1     4
## 4   S1 G2     0
## 5   S2 G2     5
## 6   S3 G2     0

一行是一个连接关系，第一列和第二列是要连接的两边，第三列是连接的强度。

2.简单画图

chordDiagram(mat)

circos.clear()
chordDiagram(df)

circos.clear()

circos.clear()是清除原来的弦图设置。你会发现颜色不一样，这是因为每次画图，颜色是随机的

3.自定义边的颜色

这些颜色出自RColorBrewer包，是我喜欢的配色，可以自己修改

library(RColorBrewer)
col = c(brewer.pal(n = 12,name = "Set3"),
        brewer.pal(n = 8,name = "Set2"))
col

##  [1] "#8DD3C7" "#FFFFB3" "#BEBADA" "#FB8072" "#80B1D3" "#FDB462" "#B3DE69"
##  [8] "#FCCDE5" "#D9D9D9" "#BC80BD" "#CCEBC5" "#FFED6F" "#66C2A5" "#FC8D62"
## [15] "#8DA0CB" "#E78AC3" "#A6D854" "#FFD92F" "#E5C494" "#B3B3B3"

border_color <- sample(col,nrow(mat)+ncol(mat)) 

chordDiagram(mat, grid.col = border_color, transparency = 0.7) 

chordDiagram(t(mat), grid.col = border_color) 

从这两张图可以看到，弦默认与行的颜色一致。

4.自定义弦的颜色

还是从刚才的颜色里面取

linkcolor <- sample(col,length(mat),replace = T)
dim(linkcolor) <- dim(mat) 
chordDiagram(mat, grid.col = border_color, col = linkcolor,transparency = 0.7) 

circos.clear()

linkcolor2 <- colorRamp2(range(mat), c("#FA0A0A", "#FFFFFF"), 
                      transparency = 0.5) # 产生连续色块并指定透明度
chordDiagram(mat, grid.col = border_color, col = linkcolor2)

circos.clear()